SAXSdb — 1dl5

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

Thermotoga maritima

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–317 Chain B； UniProt 1–317	Not recorded	CD CADMIUM ION × 9 CL CHLORIDE ION × 10 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；THREE MICROLITERS OF PROTEIN AT A CONCENTRATION OF 6.3MGS/ML IN 10MM TRIS PH 8.0, 200MM NACL, 5% GLYCEROL, LMM DTT, 5MM BME AND 0.1MM EDTA WERE MIXED WITH THREE MICROLITERS OF A RESERVOIR SOLUTION OF 28% PEG400, 100MM SODIUM ACETATE PH 4.5, AND 100MM CADMIUM CHLORIDE AND EQUILIBRATED AGAINST THE SAME., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.203
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–317 Chain B； UniProt 1–317	Not recorded	CD CADMIUM ION × 9 CL CHLORIDE ION × 10 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；THREE MICROLITERS OF PROTEIN AT A CONCENTRATION OF 6.3MGS/ML IN 10MM TRIS PH 8.0, 200MM NACL, 5% GLYCEROL, LMM DTT, 5MM BME AND 0.1MM EDTA WERE MIXED WITH THREE MICROLITERS OF A RESERVOIR SOLUTION OF 28% PEG400, 100MM SODIUM ACETATE PH 4.5, AND 100MM CADMIUM CHLORIDE AND EQUILIBRATED AGAINST THE SAME., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.203

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PIMT_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dl5
Deposition date deposition_date	1999-12-08
Structure title title	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
Keywords keywords	METHYLTRANSFERASE, ISOASPARTYL RESIDUES, PROTEIN REPAIR, DEAMIDATION, POST-TRANSLATIONAL MODIFICATION, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.33 Å
Radius of gyration Rg (electron density) rg_electron	33.98 Å
Forward intensity I(0) i0	84228400.00
Molecular weight molecular_weight	74261.0 kDa
Excluded volume excluded_volume	92937 Å³
Envelope volume envelope_volume	112070 Å³
Hydration-shell volume shell_volume	30250 Å³
Envelope diameter envelope_diameter	119.5 Å
Shell Rg shell_rg	36.33 Å
Envelope Rg envelope_rg	34.13 Å
Shape Rg shape_rg	34.01 Å
Total Rg total_rg	34.05 Å
Total atoms total_atoms	5167
Residues n_residues	633
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.3 Å
Rg (real space) rg_real	33.91 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	8.4230e+07
I(0) uncertainty (real space) i0_real_error	1.4400e+06
Rg (reciprocal space) rg_reciprocal	33.67 Å
I(0) (reciprocal space) i0_reciprocal	84210000.0000
Solution quality estimate total_estimate	0.5620
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.611
Kurtosis Kurtosis kurtosis	-0.295
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38710000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.515; Smooth: 0.434

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
Molecular weight formula_weight	36440.8 kDa
EC 编号 ec_number	2.1.1.77
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5640

MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCSI

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dl5a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.7 — Protein-L-isoaspartyl O-methyltransferase

Domain ID domain_id	d1dl5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.197 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Superfamily Superfamily superfamily	d.197.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Family Family family	d.197.1.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

Domain ID domain_id	d1dl5b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.7 — Protein-L-isoaspartyl O-methyltransferase

Domain ID domain_id	d1dl5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.197 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Superfamily Superfamily superfamily	d.197.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Family Family family	d.197.1.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1dl5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dl5A02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	20 — Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

Domain ID domain_id	1dl5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dl5B02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	20 — Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	51.060 Å
Unit-cell length b length_b	98.910 Å
Unit-cell length c length_c	76.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2030

fit	/app/data/saxs_computation/dl/1dl5/1dl5.fit
pddf	/app/data/pr_computation/dl/1dl5/1dl5.pr.out
profile	/app/data/saxs_computation/dl/1dl5/1dl5.dat

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)